rs38572

Variant names:

• chr7-76829719-T-C
• rs38572
• ENST00000648393.1:n.1020-10431A>G

Variant summary

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

The ENST00000648393.1(ENSG00000285666):​n.1020-10431A>G variant causes a intron 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: ENSG00000285666 ENST00000648393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• Publications: 2 publications found

Genes affected

ENSG00000285666 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648393.1. 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
	ENSG00000285666	ENST00000648393.1		n.1020-10431A>G		intron	N/A
	ENSG00000285666	ENST00000827560.1		n.483-3368A>G		intron	N/A
	ENSG00000285666	ENST00000827561.1		n.490-3368A>G		intron	N/A

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

African (AFR) AF: 0.0951 AC: 3819 AN: 40144

American (AMR) AF: 0.0171 AC: 256 AN: 14992

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 63 AN: 3362

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5188

South Asian (SAS) AF: 0.00901 AC: 42 AN: 4660

European-Finnish (FIN) AF: 0.0134 AC: 135 AN: 10070

Middle Eastern (MID) AF: 0.0292 AC: 8 AN: 274

European-Non Finnish (NFE) AF: 0.00854 AC: 565 AN: 66174

Other (OTH) AF: 0.0274 AC: 56 AN: 2044

Alfa AF: 0.0304 Hom.: 11

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.7
DANN	Benign	0.24
PhyloP100		0.26

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: rs38572;

hg19: chr7-76459036;