rs38572

chr7-76829719-T-C

Variant summary

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

The ENST00000648393.1(ENSG00000285666):n.1020-10431A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 147,788 control chromosomes in the GnomAD database, including 117 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 0.034 (117 hom., cov: 35)
• Consequence: ENST00000648393.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0926 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
	ENST00000648393.1	n.1020-10431A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0338 AC: 4997 AN: 147692 Hom.: 115 Cov.: 35

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.00227

Gnomad AMR AF: 0.0171

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.0142

Gnomad SAS AF: 0.00943

Gnomad FIN AF: 0.0134

Gnomad MID AF: 0.0304

Gnomad NFE AF: 0.00854

Gnomad OTH AF: 0.0277

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

GnomAD4 genome AF: 0.0339 AC: 5017 AN: 147788 Hom.: 117 Cov.: 35 AF XY: 0.0327 AC XY: 2365 AN XY: 72270

Gnomad4 AFR AF: 0.0951

Gnomad4 AMR AF: 0.0171

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.00901

Gnomad4 FIN AF: 0.0134

Gnomad4 NFE AF: 0.00854

Gnomad4 OTH AF: 0.0274

Alfa AF: 0.0304 Hom.: 11

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	4.7
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs38572; hg19: chr7-76459036;