6-77470328-T-C

Position:

• chr6-77470328-T-C

Variant summary

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

The XM_047419660.1(LOC105377864):​c.-3742-4198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,056 control chromosomes in the GnomAD database, including 35,138 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 0.66 (35138 hom., cov: 32)
• Consequence: LOC105377864 XM_047419660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977

Genes affected

LOC105377864 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377864	XM_047419660.1	c.-3742-4198T>C		intron_variant
LOC105377864	XM_047419658.1	c.-4305T>C		5_prime_UTR_variant	1/6
LOC105377864	XM_047419659.1	c.-4131T>C		5_prime_UTR_variant	2/6
LOC105377864	XM_047419661.1	c.-3916-4198T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100563 AN: 151938 Hom.: 35095 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.662 AC: 100664 AN: 152056 Hom.: 35138 Cov.: 32 AF XY: 0.660 AC XY: 49072 AN XY: 74308

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.612

Alfa AF: 0.579 Hom.: 12112

Bravo AF: 0.677

Asia WGS AF: 0.731 AC: 2541 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	0.99
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1213371; hg19: chr6-78180045;