rs211804

Variant names:

• chr7-110451403-A-C
• rs211804
• ENST00000843038.1:n.487T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-110451403-A-C
• chr7-110451403-A-G
• chr7-110451403-A-T

Variant summary

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

The ENST00000843038.1(ENSG00000226965):​n.487T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 152,114 control chromosomes in the GnomAD database, including 58,777 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 0.88 (58777 hom., cov: 32)
• Consequence: ENSG00000226965 ENST00000843038.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 1 publications found

Genes affected

ENSG00000226965 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843038.1. 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
	ENSG00000226965	ENST00000843038.1		n.487T>G		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000226965	ENST00000435466.2	TSL:4	n.328-18497T>G		intron	N/A
	ENSG00000226965	ENST00000657059.1		n.438-18497T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133449 AN: 151996 Hom.: 58730 Cov.: 32

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.878 AC: 133557 AN: 152114 Hom.: 58777 Cov.: 32 AF XY: 0.881 AC XY: 65493 AN XY: 74354

African (AFR) AF: 0.929 AC: 38542 AN: 41486

American (AMR) AF: 0.872 AC: 13306 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2768 AN: 3470

East Asian (EAS) AF: 0.942 AC: 4880 AN: 5178

South Asian (SAS) AF: 0.875 AC: 4212 AN: 4816

European-Finnish (FIN) AF: 0.904 AC: 9582 AN: 10594

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57372 AN: 67986

Other (OTH) AF: 0.869 AC: 1836 AN: 2112

Alfa AF: 0.849 Hom.: 23174

Bravo AF: 0.878

Asia WGS AF: 0.898 AC: 3119 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs211804; hg19: chr7-110091460;