rs6016596

Variant names:

• chr20-41671593-A-G
• rs6016596
• ENST00000685138.2:n.272+43861T>C

Your query was ambiguous. Multiple possible variants found:

• chr20-41671593-A-G
• chr20-41671593-A-T

Variant summary

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

The ENST00000685138.2(ENSG00000288843):​n.272+43861T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,900 control chromosomes in the GnomAD database, including 23,369 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 0.53 (23369 hom., cov: 31)
• Consequence: ENSG00000288843 ENST00000685138.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

Genes affected

ENSG00000288843 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 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
ENSG00000288843	ENST00000685138.2	n.272+43861T>C		intron_variant	Intron 1 of 1
ENSG00000288843	ENST00000686898.1	n.238-21085T>C		intron_variant	Intron 1 of 1
ENSG00000288843	ENST00000691734.1	n.356-21085T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80662 AN: 151782 Hom.: 23316 Cov.: 31

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.532 AC: 80778 AN: 151900 Hom.: 23369 Cov.: 31 AF XY: 0.535 AC XY: 39724 AN XY: 74240

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.490

Alfa AF: 0.485 Hom.: 2397

Bravo AF: 0.550

Asia WGS AF: 0.747 AC: 2598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6016596; hg19: chr20-40300232;