rs7610580

Variant names:

• chr3-178245606-A-G
• rs7610580
• ENST00000414475.1:n.104-38753T>C

Variant summary

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

The ENST00000414475.1(ENSG00000223930):​n.104-38753T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,774 control chromosomes in the GnomAD database, including 20,776 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 0.52 (20776 hom., cov: 32)
• Consequence: ENSG00000223930 ENST00000414475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18
• Publications: 2 publications found

Genes affected

ENSG00000223930 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374235	NR_188692.1	n.157-19418T>C		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223930	ENST00000414475.1	n.104-38753T>C		intron_variant	Intron 1 of 2	5
ENSG00000223930	ENST00000439810.6	n.404+32328T>C		intron_variant	Intron 3 of 7	4
ENSG00000223930	ENST00000651749.1	n.144-19418T>C		intron_variant	Intron 2 of 10

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78581 AN: 151656 Hom.: 20761 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.518 AC: 78641 AN: 151774 Hom.: 20776 Cov.: 32 AF XY: 0.515 AC XY: 38158 AN XY: 74160

African (AFR) AF: 0.612 AC: 25340 AN: 41426

American (AMR) AF: 0.464 AC: 7058 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1334 AN: 5132

South Asian (SAS) AF: 0.463 AC: 2232 AN: 4820

European-Finnish (FIN) AF: 0.466 AC: 4909 AN: 10542

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33918 AN: 67866

Other (OTH) AF: 0.527 AC: 1111 AN: 2108

Alfa AF: 0.519 Hom.: 3605

Bravo AF: 0.517

Asia WGS AF: 0.366 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.8
DANN	Benign	0.74
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs7610580; hg19: chr3-177963394;