rs4669749

Variant names:

• chr2-11552538-C-A
• rs4669749
• NM_014668.4:c.-161-3916C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-11552538-C-A
• chr2-11552538-C-G
• chr2-11552538-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014668.4(GREB1):​c.-161-3916C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,078 control chromosomes in the GnomAD database, including 38,602 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.71 (38602 hom., cov: 32)
• Consequence: GREB1 NM_014668.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 13 publications found

Genes affected

GREB1 (HGNC:24885): (growth regulating estrogen receptor binding 1) This gene is an estrogen-responsive gene that is an early response gene in the estrogen receptor-regulated pathway. It is thought to play an important role in hormone-responsive tissues and cancer. Three alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014668.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GREB1	NM_014668.4	MANE Select	c.-161-3916C>A		intron	N/A	NP_055483.2
	GREB1	NM_033090.3		c.-158-3919C>A		intron	N/A	NP_149081.1	Q4ZG55-2
	GREB1	NM_148903.3		c.-161-3916C>A		intron	N/A	NP_683701.2	Q4ZG55-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GREB1	ENST00000381486.7	TSL:5 MANE Select	c.-161-3916C>A		intron	N/A	ENSP00000370896.2	Q4ZG55-1
	GREB1	ENST00000381483.6	TSL:1	c.-158-3919C>A		intron	N/A	ENSP00000370892.2	Q4ZG55-2
	GREB1	ENST00000263834.9	TSL:1	c.-161-3916C>A		intron	N/A	ENSP00000263834.5	Q4ZG55-3

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107993 AN: 151960 Hom.: 38575 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.675

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.711 AC: 108081 AN: 152078 Hom.: 38602 Cov.: 32 AF XY: 0.717 AC XY: 53309 AN XY: 74322

African (AFR) AF: 0.725 AC: 30052 AN: 41470

American (AMR) AF: 0.660 AC: 10098 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2408 AN: 3472

East Asian (EAS) AF: 0.825 AC: 4260 AN: 5162

South Asian (SAS) AF: 0.864 AC: 4163 AN: 4818

European-Finnish (FIN) AF: 0.753 AC: 7964 AN: 10572

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46788 AN: 67980

Other (OTH) AF: 0.675 AC: 1422 AN: 2108

Alfa AF: 0.694 Hom.: 117578

Bravo AF: 0.706

Asia WGS AF: 0.824 AC: 2867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.021
DANN	Benign	0.54
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4669749; hg19: chr2-11692664;