6-78557764-T-C

Position:

• chr6-78557764-T-C

Variant summary

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

The variant allele was found at a frequency of 0.484 in 152,062 control chromosomes in the GnomAD database, including 17,956 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 0.48 (17956 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 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

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73587 AN: 151944 Hom.: 17931 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.484 AC: 73668 AN: 152062 Hom.: 17956 Cov.: 32 AF XY: 0.484 AC XY: 35999 AN XY: 74340

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.475

Alfa AF: 0.481 Hom.: 2772

Bravo AF: 0.482

Asia WGS AF: 0.335 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs623155; hg19: chr6-79267481; COSMIC: COSV69406800;