rs7627822

Variant names:

• chr3-138917970-A-C
• rs7627822
• ENST00000724700.1:n.289+2090A>C

Variant summary

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

The ENST00000724700.1(ENSG00000294607):​n.289+2090A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,060 control chromosomes in the GnomAD database, including 1,343 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 0.11 (1343 hom., cov: 32)
• Consequence: ENSG00000294607 ENST00000724700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 0 publications found

Genes affected

ENSG00000294607 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724700.1. 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
	ENSG00000294607	ENST00000724700.1		n.289+2090A>C		intron	N/A
	ENSG00000294607	ENST00000724701.1		n.252+215A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16534 AN: 151942 Hom.: 1339 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0835

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0554

Gnomad OTH AF: 0.0819

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

GnomAD4 genome AF: 0.109 AC: 16564 AN: 152060 Hom.: 1343 Cov.: 32 AF XY: 0.112 AC XY: 8325 AN XY: 74292

African (AFR) AF: 0.223 AC: 9242 AN: 41472

American (AMR) AF: 0.0577 AC: 883 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3468

East Asian (EAS) AF: 0.0839 AC: 431 AN: 5138

South Asian (SAS) AF: 0.0662 AC: 319 AN: 4820

European-Finnish (FIN) AF: 0.137 AC: 1442 AN: 10556

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0553 AC: 3763 AN: 68000

Other (OTH) AF: 0.0834 AC: 176 AN: 2110

Alfa AF: 0.0953 Hom.: 99

Bravo AF: 0.109

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7627822;

hg19: chr3-138636812;