chr6-119516757-C-G

Position:

• chr6-119516757-C-G

Variant summary

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

The ENST00000701940.1(ENSG00000287100):​n.73-33051C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,968 control chromosomes in the GnomAD database, including 27,489 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 0.60 (27489 hom., cov: 32)
• Consequence: ENST00000701940.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

Genes affected

(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 (SAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000701940.1	n.73-33051C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90497 AN: 151850 Hom.: 27458 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.596 AC: 90586 AN: 151968 Hom.: 27489 Cov.: 32 AF XY: 0.600 AC XY: 44548 AN XY: 74274

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.594

Alfa AF: 0.382 Hom.: 896

Bravo AF: 0.601

Asia WGS AF: 0.739 AC: 2571 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.85
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2036256; hg19: chr6-119837922; COSMIC: COSV69422508;