6-163984753-A-G

Variant names:

• chr6-163984753-A-G
• rs717822
• ENST00000850551.1:n.17T>C

Variant summary

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

The ENST00000850551.1(ENSG00000310515):​n.17T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,078 control chromosomes in the GnomAD database, including 7,299 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 0.30 (7299 hom., cov: 32)
• Consequence: ENSG00000310515 ENST00000850551.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 3 publications found

Genes affected

ENSG00000310515 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378102	XR_943213.4	n.558+64839A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310515	ENST00000850551.1	n.17T>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000288696	ENST00000659063.1	n.43-23771A>G		intron_variant	Intron 1 of 1
ENSG00000288696	ENST00000850151.1	n.105+57707A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46047 AN: 151960 Hom.: 7285 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.303 AC: 46104 AN: 152078 Hom.: 7299 Cov.: 32 AF XY: 0.298 AC XY: 22137 AN XY: 74374

African (AFR) AF: 0.390 AC: 16171 AN: 41490

American (AMR) AF: 0.331 AC: 5047 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1226 AN: 5156

South Asian (SAS) AF: 0.206 AC: 994 AN: 4816

European-Finnish (FIN) AF: 0.207 AC: 2192 AN: 10586

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18571 AN: 67980

Other (OTH) AF: 0.300 AC: 634 AN: 2110

Alfa AF: 0.198 Hom.: 552

Bravo AF: 0.319

Asia WGS AF: 0.220 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.065
DANN	Benign	0.21
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs717822; hg19: chr6-164405785;