ENST00000731005.1:n.279-47604T>C

Variant names:

• chr7-9807667-A-G
• rs7787204
• ENST00000731005.1:n.279-47604T>C

Variant summary

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

The ENST00000731005.1(ENSG00000295572):​n.279-47604T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0909 in 152,072 control chromosomes in the GnomAD database, including 732 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 0.091 (732 hom., cov: 33)
• Consequence: ENSG00000295572 ENST00000731005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 3 publications found

Genes affected

ENSG00000295572 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731005.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295572	ENST00000731005.1		n.279-47604T>C		intron	N/A
	ENSG00000295572	ENST00000731006.1		n.170-14109T>C		intron	N/A
	ENSG00000295572	ENST00000731007.1		n.242-47604T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0909 AC: 13812 AN: 151956 Hom.: 727 Cov.: 33

Gnomad AFR AF: 0.0715

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0962

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0791

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

GnomAD4 genome AF: 0.0909 AC: 13830 AN: 152072 Hom.: 732 Cov.: 33 AF XY: 0.0914 AC XY: 6795 AN XY: 74338

African (AFR) AF: 0.0716 AC: 2968 AN: 41480

American (AMR) AF: 0.0594 AC: 908 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0962 AC: 334 AN: 3472

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5176

South Asian (SAS) AF: 0.113 AC: 547 AN: 4822

European-Finnish (FIN) AF: 0.117 AC: 1232 AN: 10574

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7547 AN: 67962

Other (OTH) AF: 0.0821 AC: 173 AN: 2106

Alfa AF: 0.104 Hom.: 643

Bravo AF: 0.0840

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.35
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7787204; hg19: chr7-9847296;