rs7624

Variant names:

• chr19-34733565-G-A
• rs7624
• ENST00000612269.2:n.937C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-34733565-G-A
• chr19-34733565-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000612269.2(ENSG00000274104):​n.937C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,900 control chromosomes in the GnomAD database, including 6,547 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 0.28 (6547 hom., cov: 31)
  • Exomes 𝑓: 0.15 (0 hom.)
• Consequence: ENSG00000274104 ENST00000612269.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793

Genes affected

ENSG00000274104 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 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
ENSG00000274104	ENST00000612269.2	n.937C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42724 AN: 151762 Hom.: 6555 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.290

GnomAD4 exome AF: 0.150 AC: 3 AN: 20 Hom.: 0 Cov.: 0 AF XY: 0.200 AC XY: 2 AN XY: 10

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.281 AC: 42721 AN: 151880 Hom.: 6547 Cov.: 31 AF XY: 0.282 AC XY: 20946 AN XY: 74228

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.290

Alfa AF: 0.325 Hom.: 10397

Bravo AF: 0.272

Asia WGS AF: 0.254 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.96
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7624; hg19: chr19-35224470;