rs3735520

Variant names:

• chr7-81771623-G-A
• rs3735520
• ENST00000771413.1:n.118-8600G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-81771623-G-A
• chr7-81771623-G-C
• chr7-81771623-G-T

Variant summary

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

The ENST00000771413.1(ENSG00000300407):​n.118-8600G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,846 control chromosomes in the GnomAD database, including 18,330 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 (18330 hom., cov: 31)
• Consequence: ENSG00000300407 ENST00000771413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 44 publications found

Genes affected

ENSG00000300407 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 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
ENSG00000300407	ENST00000771413.1	n.118-8600G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73615 AN: 151728 Hom.: 18315 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.485 AC: 73671 AN: 151846 Hom.: 18330 Cov.: 31 AF XY: 0.482 AC XY: 35774 AN XY: 74188

African (AFR) AF: 0.587 AC: 24314 AN: 41402

American (AMR) AF: 0.461 AC: 7030 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2056 AN: 3472

East Asian (EAS) AF: 0.400 AC: 2052 AN: 5130

South Asian (SAS) AF: 0.565 AC: 2717 AN: 4808

European-Finnish (FIN) AF: 0.383 AC: 4038 AN: 10530

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29960 AN: 67926

Other (OTH) AF: 0.511 AC: 1080 AN: 2112

Alfa AF: 0.459 Hom.: 27105

Bravo AF: 0.495

Asia WGS AF: 0.482 AC: 1677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs3735520; hg19: chr7-81400939;