rs7595103

Positions:

• chr2-77848118-G-A

Variant summary

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

The NR_110288.1(LOC101927967):​n.428-8228C>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 0.667 in 152,010 control chromosomes in the GnomAD database, including 34,358 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 0.67 (34358 hom., cov: 32)
• Consequence: LOC101927967 NR_110288.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927967	NR_110288.1	n.428-8228C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000667782.1	n.222-8228C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101228 AN: 151892 Hom.: 34314 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.667 AC: 101324 AN: 152010 Hom.: 34358 Cov.: 32 AF XY: 0.673 AC XY: 49977 AN XY: 74298

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.875

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.662

Alfa AF: 0.641 Hom.: 35112

Bravo AF: 0.675

Asia WGS AF: 0.888 AC: 3083 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.51
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7595103; hg19: chr2-78075244;