6-43752256-T-C

Variant names:

• chr6-43752256-T-C
• rs4714696
• ENST00000770040.1:n.95+6287A>G

Variant summary

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

The ENST00000770040.1(ENSG00000236961):​n.95+6287A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,024 control chromosomes in the GnomAD database, including 6,193 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 0.28 (6193 hom., cov: 32)
• Consequence: ENSG00000236961 ENST00000770040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 11 publications found

Genes affected

ENSG00000236961 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 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
ENSG00000236961	ENST00000770040.1	n.95+6287A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42948 AN: 151904 Hom.: 6188 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.283 AC: 42974 AN: 152024 Hom.: 6193 Cov.: 32 AF XY: 0.282 AC XY: 20922 AN XY: 74302

African (AFR) AF: 0.279 AC: 11552 AN: 41458

American (AMR) AF: 0.341 AC: 5211 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 817 AN: 3464

East Asian (EAS) AF: 0.234 AC: 1212 AN: 5170

South Asian (SAS) AF: 0.168 AC: 811 AN: 4818

European-Finnish (FIN) AF: 0.292 AC: 3086 AN: 10568

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19367 AN: 67962

Other (OTH) AF: 0.303 AC: 639 AN: 2108

Alfa AF: 0.288 Hom.: 24353

Bravo AF: 0.293

Asia WGS AF: 0.177 AC: 617 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4714696; hg19: chr6-43719993;