rs6508962

Positions:

• chr19-28615865-G-A
• chr19-28615865-G-T

Variant summary

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

The NR_110759.1(LOC100420587):​n.656+106705C>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 0.734 in 151,412 control chromosomes in the GnomAD database, including 41,493 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 0.73 (41493 hom., cov: 28)
• Consequence: LOC100420587 NR_110759.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100420587	NR_110759.1	n.656+106705C>T		intron_variant, non_coding_transcript_variant
LOC124904681	XR_007067212.1	n.262+4859C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000585394.1	n.21-13322C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000589999.1	n.109+16755C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.733 AC: 110963 AN: 151300 Hom.: 41425 Cov.: 28

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.734 AC: 111090 AN: 151412 Hom.: 41493 Cov.: 28 AF XY: 0.730 AC XY: 54016 AN XY: 73966

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.733

Alfa AF: 0.689 Hom.: 45435

Bravo AF: 0.747

Asia WGS AF: 0.553 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6508962; hg19: chr19-29106772;