rs763672

Positions:

• chr6-74257276-G-T

Variant summary

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

The NR_110856.1(LOC101928516):​n.139-89799G>T 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 0.339 in 152,002 control chromosomes in the GnomAD database, including 10,656 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 0.34 (10656 hom., cov: 32)
• Consequence: LOC101928516 NR_110856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928516	NR_110856.1	n.139-89799G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435946.1	n.139-89799G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51600 AN: 151884 Hom.: 10658 Cov.: 32

Gnomad AFR AF: 0.0923

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.339 AC: 51603 AN: 152002 Hom.: 10656 Cov.: 32 AF XY: 0.342 AC XY: 25433 AN XY: 74270

Gnomad4 AFR AF: 0.0922

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.352

Alfa AF: 0.382 Hom.: 2119

Bravo AF: 0.325

Asia WGS AF: 0.459 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	12
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs763672; hg19: chr6-74966992;