rs42611

chr7-90320746-C-A

Variant summary

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

The NM_001384237.2(FAM237B):c.-50-19G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,258 control chromosomes in the GnomAD database, including 19,920 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 0.50 (19901 hom., cov: 33)
  • Exomes 𝑓: 0.53 (19 hom.)
• Consequence: FAM237B NM_001384237.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.89

Genes affected

FAM237B (HGNC:53217): (family with sequence similarity 237 member B)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM237B	NM_001384237.2	c.-50-19G>T		intron_variant		ENST00000692316.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM237B	ENST00000692316.1	c.-50-19G>T		intron_variant			NM_001384237.2	P1
	ENST00000445784.1	n.369+325C>A		intron_variant, non_coding_transcript_variant		1
FAM237B	ENST00000637645.2	c.-69G>T		5_prime_UTR_variant	1/2	5		P1

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75862 AN: 152020 Hom.: 19896 Cov.: 33

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.493

GnomAD4 exome AF: 0.525 AC: 63 AN: 120 Hom.: 19 Cov.: 0 AF XY: 0.511 AC XY: 46 AN XY: 90

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.545

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.499 AC: 75889 AN: 152138 Hom.: 19901 Cov.: 33 AF XY: 0.496 AC XY: 36883 AN XY: 74370

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.497

Alfa AF: 0.560 Hom.: 3033

Bravo AF: 0.479

Asia WGS AF: 0.404 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.040
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs42611; hg19: chr7-89950060; COSMIC: COSV71496282;