rs6072161

Variant names:

• chr20-40842787-T-C
• rs6072161
• ENST00000758964.1:n.86+23314A>G

Variant summary

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

The ENST00000758964.1(ENSG00000229771):​n.86+23314A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,952 control chromosomes in the GnomAD database, including 21,334 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 0.51 (21334 hom., cov: 31)
• Consequence: ENSG00000229771 ENST00000758964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.914
• Publications: 7 publications found

Genes affected

ENSG00000229771 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.602 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
ENSG00000229771	ENST00000758964.1	n.86+23314A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77986 AN: 151834 Hom.: 21317 Cov.: 31

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.514 AC: 78033 AN: 151952 Hom.: 21334 Cov.: 31 AF XY: 0.514 AC XY: 38146 AN XY: 74258

African (AFR) AF: 0.336 AC: 13897 AN: 41420

American (AMR) AF: 0.490 AC: 7487 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2364 AN: 3472

East Asian (EAS) AF: 0.281 AC: 1448 AN: 5156

South Asian (SAS) AF: 0.610 AC: 2936 AN: 4812

European-Finnish (FIN) AF: 0.656 AC: 6926 AN: 10562

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.607 AC: 41266 AN: 67946

Other (OTH) AF: 0.540 AC: 1140 AN: 2112

Alfa AF: 0.547 Hom.: 19693

Bravo AF: 0.491

Asia WGS AF: 0.443 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.6
DANN	Benign	0.87
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs6072161; hg19: chr20-39471427;