rs10249851

Positions:

• chr7-36021874-A-G

Variant summary

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

The ENST00000665884.1(ENSG00000232930):​n.386-7737A>G 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 0.061 in 152,250 control chromosomes in the GnomAD database, including 393 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 0.061 (393 hom., cov: 32)
• Consequence: ENST00000665884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20

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 = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375233	XR_927174.3	n.386-7737A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665884.1	n.386-7737A>G		intron_variant, non_coding_transcript_variant
	ENST00000667088.1	n.68+6233T>C		intron_variant, non_coding_transcript_variant
	ENST00000664385.1	n.119-7737A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0609 AC: 9266 AN: 152132 Hom.: 391 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0433

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0610 AC: 9284 AN: 152250 Hom.: 393 Cov.: 32 AF XY: 0.0599 AC XY: 4459 AN XY: 74450

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0433

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0147

Gnomad4 FIN AF: 0.0308

Gnomad4 NFE AF: 0.0433

Gnomad4 OTH AF: 0.0540

Alfa AF: 0.0466 Hom.: 252

Bravo AF: 0.0652

Asia WGS AF: 0.0160 AC: 54 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	0.10
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10249851; hg19: chr7-36061484;