rs7610580

chr3-178245606-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651749.1(ENSG00000223930):n.144-19418T>C variant causes a intron, non coding transcript 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: ENST00000651749.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651749.1	n.144-19418T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.527

Alfa AF: 0.517 Hom.: 3464

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7610580; hg19: chr3-177963394;