rs737714

Variant names:

• chr7-9147664-G-A
• rs737714
• ENST00000612945.4:n.209+41913C>T

Variant summary

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

The ENST00000612945.4(ENSG00000278254):​n.209+41913C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,762 control chromosomes in the GnomAD database, including 15,431 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 0.43 (15431 hom., cov: 32)
• Consequence: ENSG00000278254 ENST00000612945.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773
• Publications: 3 publications found

Genes affected

ENSG00000278254 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 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
ENSG00000278254	ENST00000612945.4	n.209+41913C>T		intron_variant	Intron 1 of 1	1
ENSG00000278254	ENST00000613936.6	n.273+41896C>T		intron_variant	Intron 1 of 1	1
ENSG00000278254	ENST00000614137.1	n.299-4741C>T		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65052 AN: 151644 Hom.: 15410 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.429 AC: 65124 AN: 151762 Hom.: 15431 Cov.: 32 AF XY: 0.421 AC XY: 31200 AN XY: 74174

African (AFR) AF: 0.637 AC: 26363 AN: 41400

American (AMR) AF: 0.381 AC: 5787 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1699 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1647 AN: 5144

South Asian (SAS) AF: 0.260 AC: 1254 AN: 4828

European-Finnish (FIN) AF: 0.288 AC: 3029 AN: 10532

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24084 AN: 67884

Other (OTH) AF: 0.430 AC: 902 AN: 2100

Alfa AF: 0.389 Hom.: 7646

Bravo AF: 0.447

Asia WGS AF: 0.299 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.54
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs737714; hg19: chr7-9187294;