6-31449143-C-G

Variant names:

• chr6-31449143-C-G
• rs16899646
• ENST00000673857.1:n.63-13980C>G

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-13980C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 151,334 control chromosomes in the GnomAD database, including 3,495 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 0.19 (3495 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 17 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 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
ENSG00000288587	ENST00000673857.1	n.63-13980C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29130 AN: 151218 Hom.: 3489 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.193 AC: 29174 AN: 151334 Hom.: 3495 Cov.: 31 AF XY: 0.198 AC XY: 14657 AN XY: 73950

African (AFR) AF: 0.278 AC: 11437 AN: 41082

American (AMR) AF: 0.266 AC: 4029 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3468

East Asian (EAS) AF: 0.170 AC: 871 AN: 5120

South Asian (SAS) AF: 0.197 AC: 943 AN: 4798

European-Finnish (FIN) AF: 0.223 AC: 2348 AN: 10512

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.118 AC: 7985 AN: 67916

Other (OTH) AF: 0.198 AC: 415 AN: 2096

Alfa AF: 0.0707 Hom.: 99

Bravo AF: 0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.72
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs16899646; hg19: chr6-31416920;