rs7607316

Variant names:

• chr2-236613199-C-A
• rs7607316
• ENST00000779927.1:n.311+14991C>A

Variant summary

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

The ENST00000779927.1(ENSG00000301575):​n.311+14991C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,952 control chromosomes in the GnomAD database, including 10,075 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 0.31 (10075 hom., cov: 32)
• Consequence: ENSG00000301575 ENST00000779927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• Publications: 8 publications found

Genes affected

ENSG00000301575 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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
ENSG00000301575	ENST00000779927.1	n.311+14991C>A		intron_variant	Intron 2 of 2
ENSG00000301575	ENST00000779928.1	n.122+27795C>A		intron_variant	Intron 1 of 1
ENSG00000301575	ENST00000779929.1	n.238+14991C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47722 AN: 151834 Hom.: 10040 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.315 AC: 47800 AN: 151952 Hom.: 10075 Cov.: 32 AF XY: 0.309 AC XY: 22932 AN XY: 74278

African (AFR) AF: 0.604 AC: 25018 AN: 41396

American (AMR) AF: 0.207 AC: 3161 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 813 AN: 3472

East Asian (EAS) AF: 0.138 AC: 712 AN: 5154

South Asian (SAS) AF: 0.265 AC: 1272 AN: 4800

European-Finnish (FIN) AF: 0.153 AC: 1617 AN: 10582

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14207 AN: 67956

Other (OTH) AF: 0.309 AC: 651 AN: 2110

Alfa AF: 0.252 Hom.: 11151

Bravo AF: 0.331

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.079
DANN	Benign	0.44
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs7607316; hg19: chr2-237521842;