rs7624

Positions:

• 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: ENST00000612269.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000612269.2	n.937C>T		non_coding_transcript_exon_variant	1/1

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;