rs7319671

Variant names:

• chr13-37451087-A-G
• rs7319671
• ENST00000827669.1:n.223-27518A>G

Variant summary

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

The ENST00000827669.1(ENSG00000307651):​n.223-27518A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,014 control chromosomes in the GnomAD database, including 10,832 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 0.36 (10832 hom., cov: 32)
• Consequence: ENSG00000307651 ENST00000827669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 4 publications found

Genes affected

ENSG00000307651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827669.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307651	ENST00000827669.1		n.223-27518A>G		intron	N/A
	ENSG00000307651	ENST00000827670.1		n.274-5565A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55366 AN: 151896 Hom.: 10807 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.365 AC: 55435 AN: 152014 Hom.: 10832 Cov.: 32 AF XY: 0.368 AC XY: 27369 AN XY: 74280

African (AFR) AF: 0.471 AC: 19507 AN: 41432

American (AMR) AF: 0.411 AC: 6277 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1237 AN: 3466

East Asian (EAS) AF: 0.501 AC: 2589 AN: 5164

South Asian (SAS) AF: 0.558 AC: 2686 AN: 4810

European-Finnish (FIN) AF: 0.248 AC: 2623 AN: 10574

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19388 AN: 67980

Other (OTH) AF: 0.371 AC: 786 AN: 2116

Alfa AF: 0.340 Hom.: 1209

Bravo AF: 0.379

Asia WGS AF: 0.536 AC: 1864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		-0.22

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7319671;

hg19: chr13-38025224;

COSMIC: COSV69347178;