rs621054

Variant names:

• chr7-64357798-T-G
• rs621054
• ENST00000752301.1:n.80+13335A>C

Variant summary

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

The ENST00000752301.1(ENSG00000287699):​n.80+13335A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 82,416 control chromosomes in the GnomAD database, including 6,355 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 0.49 (6355 hom., cov: 21)
• Consequence: ENSG00000287699 ENST00000752301.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 1 publications found

Genes affected

ENSG00000287699 (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 (NFE) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287699	ENST00000752301.1	n.80+13335A>C		intron_variant	Intron 1 of 2
ENSG00000287699	ENST00000752302.1	n.50+13335A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.487 AC: 40162 AN: 82384 Hom.: 6351 Cov.: 21

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.487 AC: 40168 AN: 82416 Hom.: 6355 Cov.: 21 AF XY: 0.482 AC XY: 19518 AN XY: 40464

African (AFR) AF: 0.303 AC: 3730 AN: 12324

American (AMR) AF: 0.457 AC: 4225 AN: 9236

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 976 AN: 2004

East Asian (EAS) AF: 0.507 AC: 1538 AN: 3034

South Asian (SAS) AF: 0.525 AC: 1891 AN: 3602

European-Finnish (FIN) AF: 0.459 AC: 2759 AN: 6012

Middle Eastern (MID) AF: 0.570 AC: 114 AN: 200

European-Non Finnish (NFE) AF: 0.543 AC: 24101 AN: 44376

Other (OTH) AF: 0.523 AC: 628 AN: 1200

Alfa AF: 0.296 Hom.: 971

Bravo AF: 0.253

Asia WGS AF: 0.281 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.3
DANN	Benign	0.37
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs621054; hg19: chr7-63818176;